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yhoogstrate / flaimapper

:honeybee: Fragment Location Annotation Identification Mapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data
GNU General Public License v3.0
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indexing Fa file results in a warning in STDERR #1

Closed yhoogstrate closed 9 years ago

yhoogstrate commented 9 years ago

The function:

pysam.Fastafile(args.fasta) (flaimapper bin, line 80)

Gives a warning if the fasta file has no corresponding faid index: [fai_load] build FASTA index. . This warning should be send to stdout.

Suggested solution is to 'manually' index it before sending it through the pysam function, but it remains unclear how to call this index function from the pysam library.

yhoogstrate commented 9 years ago

This issue has been solved in v1.1.4 but a similar issue has appeared:

the following "Indexing BAM file with samtools: /data/galaxy/galaxy-dist/database/files/002/dataset_2337.dat"

is being send to stderr but should be send to stdout

yhoogstrate commented 9 years ago

This issue has been solved in v1.1.5