lncLOOM
commented
3 years ago Hi,
This was a small problem with python3, in the lincRNA_Annotate.py script. The code has been updated in the github LncLOOMv2 folder, and should work now. Please let me know if there is still a problem.
From: smej20 @.> Sent: Thursday, June 3, 2021 11:33 AM To: lncLOOM/LncLOOMv2 @.> Cc: Subscribed @.***> Subject: [lncLOOM/LncLOOMv2] eCLIP ANNOTATION ERROR! 'map' object is not subscriptable (#2)
Hi, I'm getting an error when trying to run my code against the eclip data and not quite sure what this means. I've tried re-downloading the supplied hg19.fa and eclip data but still no luck.
LncLOOM =========================== Ulitsky Lab - Weizmann Institute of Science =========================== Graph-based framework to mine ordered combinations of short conserved kmers in lincRNA sequences
============================================================== INPUT ARGUMENTS VALID...STARTING PROGRAM...
Excluding identical sequences...
FASTA FILE PARSED: Total sequences extracted = 9 Longest sequence = 7039 bases Shortest sequence = 963 bases
Building a new DB, current time: 06/03/2021 10:24:41 New DB name: /Users/Steph/LncLOOMv2/LncLOOMv2/LincMotif/Run_Files/Blast/Sequences_BLAST_DBmain New DB title: ./LincMotif/Run_Files/Sequences.fasta Sequence type: Nucleotide Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 9 sequences in 0.008605 seconds.
============================================================== BLAST SUCCESSFUL - SEQUENCES ORDERD BY HOMOLOGY...
NO CONSTRAINTS IMPOSED ON GRAPH CONSTRUCTION...
Building graph...kmer length = 15 Building graph...kmer length = 14 Building graph...kmer length = 13 Building graph...kmer length = 12 Building graph...kmer length = 11 Building graph...kmer length = 10 Building graph...kmer length = 9 Building graph...kmer length = 8 Building graph...kmer length = 7 Building graph...kmer length = 6 Refining Graph... FINAL GRAPH RETURNED Number of nodes = 1331 Number of edges = 698
============================================================== MOTIFS DISCOVERY SUCCESSFUL
Running BLAT Loaded 3095693983 letters in 25 sequences Searched 2315 bases in 1 sequences eCLIP ANNOTATION ERROR! 'map' object is not subscriptable Writing Pre-HTML Result (prior to statistical analysis)...
===================================================================================================
LncLOOM COMPLETE
Any suggestions/help would be much appreciated! Many thanks!
Best, Steph
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smej20
Hi, I'm getting an error when trying to run my code against the eclip data and not quite sure what this means. I've tried re-downloading the supplied hg19.fa and eclip data but still no luck.
LncLOOM
=========================== Ulitsky Lab - Weizmann Institute of Science =========================== Graph-based framework to mine ordered combinations of short conserved kmers in lincRNA sequences
============================================================== INPUT ARGUMENTS VALID...STARTING PROGRAM...
Excluding identical sequences...
FASTA FILE PARSED: Total sequences extracted = 9 Longest sequence = 7039 bases Shortest sequence = 963 bases
Building a new DB, current time: 06/03/2021 10:24:41 New DB name: /Users/Steph/LncLOOMv2/LncLOOMv2/LincMotif/Run_Files/Blast/Sequences_BLAST_DBmain New DB title: ./LincMotif/Run_Files/Sequences.fasta Sequence type: Nucleotide Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 9 sequences in 0.008605 seconds.
============================================================== BLAST SUCCESSFUL - SEQUENCES ORDERD BY HOMOLOGY...
NO CONSTRAINTS IMPOSED ON GRAPH CONSTRUCTION...
Building graph...kmer length = 15 Building graph...kmer length = 14 Building graph...kmer length = 13 Building graph...kmer length = 12 Building graph...kmer length = 11 Building graph...kmer length = 10 Building graph...kmer length = 9 Building graph...kmer length = 8 Building graph...kmer length = 7 Building graph...kmer length = 6 Refining Graph... FINAL GRAPH RETURNED Number of nodes = 1331 Number of edges = 698
============================================================== MOTIFS DISCOVERY SUCCESSFUL
Running BLAT Loaded 3095693983 letters in 25 sequences Searched 2315 bases in 1 sequences eCLIP ANNOTATION ERROR! 'map' object is not subscriptable Writing Pre-HTML Result (prior to statistical analysis)...
===================================================================================================
LncLOOM COMPLETE
Any suggestions/help would be much appreciated! Many thanks!
Best, Steph