search

simon-anders / htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
https://htseq.readthedocs.io/en/release_0.11.1/
GNU General Public License v3.0
122 stars 77 forks source link

--nonunique all #54

Closed dws23 closed 6 years ago

dws23 commented 6 years ago

Hi, I have been trying to get the counts for features that are very close together, but reads will likely overlap (ChIP-seq, not RNA). I have been having errors when I try to use the --nonunique option. This is the error I get:

$ htseq-count -f bam -r pos -s reverse -t transcript -i transcript_id --nonunique-all ARPE19_ChIP_Control01.final.sorted.bam /projects/scratch/skcm/ARPE19/RNA/Homo_sapiens.GRCh38.90.gtf >> Control_01.reverse.transcript.counts.txt

Usage: htseq-count [options] alignment_file gff_file

htseq-count: error: no such option: --nonunique-all

I have tried updating my version with pip install --upgrade HTSeq, but I am still getting the error. I am using Python 2.7.3.

Is there a solution for this?

Thank you,

Dave

iosonofabio commented 6 years ago

Sorry what version of htseq are you using?

On May 11, 2018 4:27:22 PM PDT, dws23 notifications@github.com wrote:

Hi, I have been trying to get the counts for features that are very close together, but reads will likely overlap (ChIP-seq, not RNA). I have been having errors when I try to use the --nonunique option. This is the error I get:

$ htseq-count -f bam -r pos -s reverse -t transcript -i transcript_id --nonunique-all ARPE19_ChIP_Control01.final.sorted.bam /projects/scratch/skcm/ARPE19/RNA/Homo_sapiens.GRCh38.90.gtf >> Control_01.reverse.transcript.counts.txt

Usage: htseq-count [options] alignment_file gff_file

htseq-count: error: no such option: --nonunique-all

I have tried updating my version with pip install --upgrade HTSeq, but I am still getting the error. I am using Python 2.7.3.

Is there a solution for this?

Thank you,

Dave

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/simon-anders/htseq/issues/54

iosonofabio commented 6 years ago

BTW there's no dash btw "--nonunique" and "all"

On May 11, 2018 4:27:22 PM PDT, dws23 notifications@github.com wrote:

Hi, I have been trying to get the counts for features that are very close together, but reads will likely overlap (ChIP-seq, not RNA). I have been having errors when I try to use the --nonunique option. This is the error I get:

$ htseq-count -f bam -r pos -s reverse -t transcript -i transcript_id --nonunique-all ARPE19_ChIP_Control01.final.sorted.bam /projects/scratch/skcm/ARPE19/RNA/Homo_sapiens.GRCh38.90.gtf >> Control_01.reverse.transcript.counts.txt

Usage: htseq-count [options] alignment_file gff_file

htseq-count: error: no such option: --nonunique-all

I have tried updating my version with pip install --upgrade HTSeq, but I am still getting the error. I am using Python 2.7.3.

Is there a solution for this?

Thank you,

Dave

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/simon-anders/htseq/issues/54

dws23 commented 6 years ago

Hi, thank you for the quick response. I thought it was update to 0.9.0, I did this using pip upgrade, but it said the version was current.

login4->[/projects/scratch/skcm/ARPE19/RNA]$ pip install HTSeq Requirement already satisfied (use --upgrade to upgrade): HTSeq in /nethome/dws23/VirtualPython/ENV/lib/python2.7/site-packages Requirement already satisfied (use --upgrade to upgrade): numpy in /nethome/dws23/VirtualPython/ENV/lib/python2.7/site-packages (from HTSeq) Requirement already satisfied (use --upgrade to upgrade): pysam>=0.9.0 in /nethome/dws23/VirtualPython/ENV/lib/python2.7/site-packages (from HTSeq) You are using pip version 8.1.2, however version 10.0.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. login4->[/projects/scratch/skcm/ARPE19/RNA]$ pip install --upgrade HTSeq Requirement already up-to-date: HTSeq in /nethome/dws23/VirtualPython/ENV/lib/python2.7/site-packages

But when I run the prompt with no options, it says version 0.6.0

login4->[/projects/scratch/skcm/ARPE19/RNA]$ htseq-count Usage: htseq-count [options] alignment_file gff_file

This script takes an alignment file in SAM/BAM format and a feature file in GFF format and calculates for each feature the number of reads mapping to it. See http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.

Options: -h, --help show this help message and exit -f SAMTYPE, --format=SAMTYPE type of data, either 'sam' or 'bam' (default: sam) -r ORDER, --order=ORDER 'pos' or 'name'. Sorting order of (default: name). Paired-end sequencing data must be sorted either by position or by read name, and the sorting order must be specified. Ignored for single- end data. -s STRANDED, --stranded=STRANDED whether the data is from a strand-specific assay. Specify 'yes', 'no', or 'reverse' (default: yes). 'reverse' means 'yes' with reversed strand interpretation -a MINAQUAL, --minaqual=MINAQUAL skip all reads with alignment quality lower than the given minimum value (default: 10) -t FEATURETYPE, --type=FEATURETYPE feature type (3rd column in GFF file) to be used, all features of other type are ignored (default, suitable for Ensembl GTF files: exon) -i IDATTR, --idattr=IDATTR GFF attribute to be used as feature ID (default, suitable for Ensembl GTF files: gene_id) -m MODE, --mode=MODE mode to handle reads overlapping more than one feature (choices: union, intersection-strict, intersection- nonempty; default: union) -o SAMOUT, --samout=SAMOUT write out all SAM alignment records into an output SAM file called SAMOUT, annotating each line with its feature assignment (as an optional field with tag 'XF') -q, --quiet suppress progress report

Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General Public License v3. Part of the 'HTSeq' framework, version 0.6.0.

I did not have a dash between nonunique and all, but I tried that too just in case. And I tried it with no space, and a –n, etc. Everything I could think of.

login4->[/projects/scratch/skcm/ARPE19/RNA]$ htseq-count -f bam -r pos -s reverse -t transcript -i transcript_id --nonunique all ARPE19_RNA_Control01.starAli.90.gtf >> Control_01.reverse.transcript.counts.txt Usage: htseq-count [options] alignment_file gff_file

htseq-count: error: no such option: --nonunique

Thank you,

Dave

From: Fabio Zanini [mailto:notifications@github.com] Sent: Friday, May 11, 2018 10:38 PM To: simon-anders/htseq htseq@noreply.github.com Cc: Sant, David Wayne dws23@med.miami.edu; Author author@noreply.github.com Subject: Re: [simon-anders/htseq] --nonunique all (#54)

Sorry what version of htseq are you using?

On May 11, 2018 4:27:22 PM PDT, dws23 notifications@github.com<mailto:notifications@github.com> wrote:

Hi, I have been trying to get the counts for features that are very close together, but reads will likely overlap (ChIP-seq, not RNA). I have been having errors when I try to use the --nonunique option. This is the error I get:

$ htseq-count -f bam -r pos -s reverse -t transcript -i transcript_id --nonunique-all ARPE19_ChIP_Control01.final.sorted.bam /projects/scratch/skcm/ARPE19/RNA/Homo_sapiens.GRCh38.90.gtf >> Control_01.reverse.transcript.counts.txt

Usage: htseq-count [options] alignment_file gff_file

htseq-count: error: no such option: --nonunique-all

I have tried updating my version with pip install --upgrade HTSeq, but I am still getting the error. I am using Python 2.7.3.

Is there a solution for this?

Thank you,

Dave

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/simon-anders/htseq/issues/54

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsimon-anders%2Fhtseq%2Fissues%2F54%23issuecomment-388524253&data=02%7C01%7Cdws23%40med.miami.edu%7C5f80acbce4094220699e08d5b7b167c9%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636616894939229418&sdata=eSpa0w6atNDAiGx87P8FuzJgHTjDN4wSCL10uhGdW70%3D&reserved=0, or mute the threadhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAO86FCgXWrq5qcBx7S-rRfaKIbgIB9rjks5txksTgaJpZM4T8LY4&data=02%7C01%7Cdws23%40med.miami.edu%7C5f80acbce4094220699e08d5b7b167c9%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636616894939229418&sdata=aFsTLVkhMrFT18dISWolc094EmUzrc6ifkRdw0USvJk%3D&reserved=0.

iosonofabio commented 6 years ago

That's not how pip works, please read the pip manual. Upgrade htseq and it'll work

pip install HTSeq==0.10.0

Cheers Fabio

On May 11, 2018 7:51:47 PM PDT, dws23 notifications@github.com wrote:

Hi, thank you for the quick response. I thought it was update to 0.9.0, I did this using pip upgrade, but it said the version was current.

login4->[/projects/scratch/skcm/ARPE19/RNA]$ pip install HTSeq Requirement already satisfied (use --upgrade to upgrade): HTSeq in /nethome/dws23/VirtualPython/ENV/lib/python2.7/site-packages Requirement already satisfied (use --upgrade to upgrade): numpy in /nethome/dws23/VirtualPython/ENV/lib/python2.7/site-packages (from HTSeq) Requirement already satisfied (use --upgrade to upgrade): pysam>=0.9.0 in /nethome/dws23/VirtualPython/ENV/lib/python2.7/site-packages (from HTSeq) You are using pip version 8.1.2, however version 10.0.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. login4->[/projects/scratch/skcm/ARPE19/RNA]$ pip install --upgrade HTSeq Requirement already up-to-date: HTSeq in /nethome/dws23/VirtualPython/ENV/lib/python2.7/site-packages

But when I run the prompt with no options, it says version 0.6.0

login4->[/projects/scratch/skcm/ARPE19/RNA]$ htseq-count Usage: htseq-count [options] alignment_file gff_file

This script takes an alignment file in SAM/BAM format and a feature file in GFF format and calculates for each feature the number of reads mapping to it. See http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.

Options: -h, --help show this help message and exit -f SAMTYPE, --format=SAMTYPE type of data, either 'sam' or 'bam' (default: sam) -r ORDER, --order=ORDER 'pos' or 'name'. Sorting order of (default: name). Paired-end sequencing data must be sorted either by position or by read name, and the sorting order must be specified. Ignored for single- end data. -s STRANDED, --stranded=STRANDED whether the data is from a strand-specific assay. Specify 'yes', 'no', or 'reverse' (default: yes). 'reverse' means 'yes' with reversed strand interpretation -a MINAQUAL, --minaqual=MINAQUAL skip all reads with alignment quality lower than the given minimum value (default: 10) -t FEATURETYPE, --type=FEATURETYPE feature type (3rd column in GFF file) to be used, all features of other type are ignored (default, suitable for Ensembl GTF files: exon) -i IDATTR, --idattr=IDATTR GFF attribute to be used as feature ID (default, suitable for Ensembl GTF files: gene_id) -m MODE, --mode=MODE mode to handle reads overlapping more than one feature (choices: union, intersection-strict, intersection- nonempty; default: union) -o SAMOUT, --samout=SAMOUT write out all SAM alignment records into an output SAM file called SAMOUT, annotating each line with its feature assignment (as an optional field with tag 'XF') -q, --quiet suppress progress report

Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General Public License v3. Part of the 'HTSeq' framework, version 0.6.0.

I did not have a dash between nonunique and all, but I tried that too just in case. And I tried it with no space, and a –n, etc. Everything I could think of.

login4->[/projects/scratch/skcm/ARPE19/RNA]$ htseq-count -f bam -r pos -s reverse -t transcript -i transcript_id --nonunique all ARPE19_RNA_Control01.starAli.90.gtf >> Control_01.reverse.transcript.counts.txt Usage: htseq-count [options] alignment_file gff_file

htseq-count: error: no such option: --nonunique

Thank you,

Dave

From: Fabio Zanini [mailto:notifications@github.com] Sent: Friday, May 11, 2018 10:38 PM To: simon-anders/htseq htseq@noreply.github.com Cc: Sant, David Wayne dws23@med.miami.edu; Author author@noreply.github.com Subject: Re: [simon-anders/htseq] --nonunique all (#54)

Sorry what version of htseq are you using?

On May 11, 2018 4:27:22 PM PDT, dws23 notifications@github.com<mailto:notifications@github.com> wrote:

Hi, I have been trying to get the counts for features that are very close together, but reads will likely overlap (ChIP-seq, not RNA). I have been having errors when I try to use the --nonunique option. This is the error I get:

$ htseq-count -f bam -r pos -s reverse -t transcript -i transcript_id --nonunique-all ARPE19_ChIP_Control01.final.sorted.bam /projects/scratch/skcm/ARPE19/RNA/Homo_sapiens.GRCh38.90.gtf >> Control_01.reverse.transcript.counts.txt

Usage: htseq-count [options] alignment_file gff_file

htseq-count: error: no such option: --nonunique-all

I have tried updating my version with pip install --upgrade HTSeq, but I am still getting the error. I am using Python 2.7.3.

Is there a solution for this?

Thank you,

Dave

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/simon-anders/htseq/issues/54

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsimon-anders%2Fhtseq%2Fissues%2F54%23issuecomment-388524253&data=02%7C01%7Cdws23%40med.miami.edu%7C5f80acbce4094220699e08d5b7b167c9%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636616894939229418&sdata=eSpa0w6atNDAiGx87P8FuzJgHTjDN4wSCL10uhGdW70%3D&reserved=0, or mute the threadhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAO86FCgXWrq5qcBx7S-rRfaKIbgIB9rjks5txksTgaJpZM4T8LY4&data=02%7C01%7Cdws23%40med.miami.edu%7C5f80acbce4094220699e08d5b7b167c9%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636616894939229418&sdata=aFsTLVkhMrFT18dISWolc094EmUzrc6ifkRdw0USvJk%3D&reserved=0.

-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/simon-anders/htseq/issues/54#issuecomment-388524902

dws23 commented 6 years ago

Oh, ok. Thank you.

Sent from my iPhone

On May 11, 2018, at 11:12 PM, Fabio Zanini notifications@github.com<mailto:notifications@github.com> wrote:

That's not how pip works, please read the pip manual. Upgrade htseq and it'll work

pip install HTSeq==0.10.0

Cheers Fabio

On May 11, 2018 7:51:47 PM PDT, dws23 notifications@github.com<mailto:notifications@github.com> wrote:

Hi, thank you for the quick response. I thought it was update to 0.9.0, I did this using pip upgrade, but it said the version was current.

login4->[/projects/scratch/skcm/ARPE19/RNA]$ pip install HTSeq Requirement already satisfied (use --upgrade to upgrade): HTSeq in /nethome/dws23/VirtualPython/ENV/lib/python2.7/site-packages Requirement already satisfied (use --upgrade to upgrade): numpy in /nethome/dws23/VirtualPython/ENV/lib/python2.7/site-packages (from HTSeq) Requirement already satisfied (use --upgrade to upgrade): pysam>=0.9.0 in /nethome/dws23/VirtualPython/ENV/lib/python2.7/site-packages (from HTSeq) You are using pip version 8.1.2, however version 10.0.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. login4->[/projects/scratch/skcm/ARPE19/RNA]$ pip install --upgrade HTSeq Requirement already up-to-date: HTSeq in /nethome/dws23/VirtualPython/ENV/lib/python2.7/site-packages

But when I run the prompt with no options, it says version 0.6.0

login4->[/projects/scratch/skcm/ARPE19/RNA]$ htseq-count Usage: htseq-count [options] alignment_file gff_file

This script takes an alignment file in SAM/BAM format and a feature file in GFF format and calculates for each feature the number of reads mapping to it. See http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.

Options: -h, --help show this help message and exit -f SAMTYPE, --format=SAMTYPE type of data, either 'sam' or 'bam' (default: sam) -r ORDER, --order=ORDER 'pos' or 'name'. Sorting order of (default: name). Paired-end sequencing data must be sorted either by position or by read name, and the sorting order must be specified. Ignored for single- end data. -s STRANDED, --stranded=STRANDED whether the data is from a strand-specific assay. Specify 'yes', 'no', or 'reverse' (default: yes). 'reverse' means 'yes' with reversed strand interpretation -a MINAQUAL, --minaqual=MINAQUAL skip all reads with alignment quality lower than the given minimum value (default: 10) -t FEATURETYPE, --type=FEATURETYPE feature type (3rd column in GFF file) to be used, all features of other type are ignored (default, suitable for Ensembl GTF files: exon) -i IDATTR, --idattr=IDATTR GFF attribute to be used as feature ID (default, suitable for Ensembl GTF files: gene_id) -m MODE, --mode=MODE mode to handle reads overlapping more than one feature (choices: union, intersection-strict, intersection- nonempty; default: union) -o SAMOUT, --samout=SAMOUT write out all SAM alignment records into an output SAM file called SAMOUT, annotating each line with its feature assignment (as an optional field with tag 'XF') -q, --quiet suppress progress report

Written by Simon Anders (sanders@fs.tum.demailto:sanders@fs.tum.de), European Molecular Biology Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General Public License v3. Part of the 'HTSeq' framework, version 0.6.0.

I did not have a dash between nonunique and all, but I tried that too just in case. And I tried it with no space, and a –n, etc. Everything I could think of.

login4->[/projects/scratch/skcm/ARPE19/RNA]$ htseq-count -f bam -r pos -s reverse -t transcript -i transcript_id --nonunique all ARPE19_RNA_Control01.starAli.90.gtf >> Control_01.reverse.transcript.counts.txt Usage: htseq-count [options] alignment_file gff_file

htseq-count: error: no such option: --nonunique

Thank you,

Dave

From: Fabio Zanini [mailto:notifications@github.com] Sent: Friday, May 11, 2018 10:38 PM To: simon-anders/htseq htseq@noreply.github.com<mailto:htseq@noreply.github.com> Cc: Sant, David Wayne dws23@med.miami.edu<mailto:dws23@med.miami.edu>; Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [simon-anders/htseq] --nonunique all (#54)

Sorry what version of htseq are you using?

On May 11, 2018 4:27:22 PM PDT, dws23 notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Hi, I have been trying to get the counts for features that are very close together, but reads will likely overlap (ChIP-seq, not RNA). I have been having errors when I try to use the --nonunique option. This is the error I get:

$ htseq-count -f bam -r pos -s reverse -t transcript -i transcript_id --nonunique-all ARPE19_ChIP_Control01.final.sorted.bam /projects/scratch/skcm/ARPE19/RNA/Homo_sapiens.GRCh38.90.gtf >> Control_01.reverse.transcript.counts.txt

Usage: htseq-count [options] alignment_file gff_file

htseq-count: error: no such option: --nonunique-all

I have tried updating my version with pip install --upgrade HTSeq, but I am still getting the error. I am using Python 2.7.3.

Is there a solution for this?

Thank you,

Dave

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/simon-anders/htseq/issues/54

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsimon-anders%2Fhtseq%2Fissues%2F54%23issuecomment-388524253&data=02%7C01%7Cdws23%40med.miami.edu%7C5f80acbce4094220699e08d5b7b167c9%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636616894939229418&sdata=eSpa0w6atNDAiGx87P8FuzJgHTjDN4wSCL10uhGdW70%3D&reserved=0, or mute the threadhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAO86FCgXWrq5qcBx7S-rRfaKIbgIB9rjks5txksTgaJpZM4T8LY4&data=02%7C01%7Cdws23%40med.miami.edu%7C5f80acbce4094220699e08d5b7b167c9%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636616894939229418&sdata=aFsTLVkhMrFT18dISWolc094EmUzrc6ifkRdw0USvJk%3D&reserved=0.

-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/simon-anders/htseq/issues/54#issuecomment-388524902

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsimon-anders%2Fhtseq%2Fissues%2F54%23issuecomment-388525915&data=02%7C01%7Cdws23%40med.miami.edu%7C89771b796b9e485bddf808d5b7b64104%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636616915763741198&sdata=O3%2FkULZgbVd1ViwJ%2Bs86%2BiIR%2Bt%2BUCiAyZozX7ywHRLc%3D&reserved=0, or mute the threadhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAO86FI_CNtDztpRxTVVMj0SH-6W7qIT-ks5txlM1gaJpZM4T8LY4&data=02%7C01%7Cdws23%40med.miami.edu%7C89771b796b9e485bddf808d5b7b64104%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636616915763741198&sdata=TeZderS1m1%2FMEGbZYJnbcy8uF%2Bx22qDtMRp7HekMchw%3D&reserved=0.