Format Of Pathway File For Genome Music: Error Upon Running

Question

[DoubleD]

Hello,

I have created a pathway file from the KEGG database and believe that I have it formatted correctly (per the geno music help files). However, when I run "genome music path-scan etc" I get the following error

Argument "gene_line" isn't numeric in numeric eq (==) at /usr/share/perl5/Genome/Model/Tools/Music/PathScan.pm line 258, <GEN5> line 1.
Use of uninitialized value $gene_symbol in hash element at /usr/share/perl5/Genome/Model/Tools/Music/PathScan.pm line 263, <GEN5> line 1.
Use of uninitialized value $gene_symbol in hash element at /usr/share/perl5/Genome/Model/Tools/Music/PathScan.pm line 263, <GEN5> line 1.
Use of uninitialized value $gene in hash element at /usr/share/perl5/Genome/Model/Tools/Music/PathScan.pm line 320.
ERROR: Can't call method "print" on an undefined value at /usr/share/perl5/Genome/Model/Tools/Music/PathScan.pm line 403.

This is the output after it Skips a number of genes as being unknown. I have checked over the pathway file and the format appears to be correct, with the entrez ID followed by the gene_name, a : in between and a | separating each.

path_id    path_name    class    gene_line    diseases    drugs    description
hsa02010    KEGG_ABC_TRANSPORTERS    Membrane transport    10347:ABCA7|64137:ABCG4|215:ABCD1|94160:ABCC12|19:ABCA1|6891:TAP2|23460:ABCA6|6890:TAP1|23461:ABCA5|11194:ABCB8|10349:ABCA10|5826:ABCD4|21:ABCA3|8647:ABCB11|5825:ABCD3|20:ABCA2|1244:ABCC2|85320:ABCC11|368:ABCC6|8714:ABCC3|10060:ABCC9|9429:ABCG2|10257:ABCC4|10057:ABCC5|26154:ABCA12|9619:ABCG1|5244:ABCB4|1080:CFTR|5243:ABCB1|4363:ABCC1|225:ABCD2|10058:ABCB6|22:ABCB7|10351:ABCA8|24:ABCA4|6833:ABCC8|89845:ABCC10|23456:ABCB10|23457:ABCB9|154664:ABCA13|10350:ABCA9|340273:ABCB5|64240:ABCG5|64241:ABCG8            
hsa05221    KEGG_ACUTE_MYELOID_LEUKEMIA    Cancers    6655:SOS2|1147:CHUK|6774:STAT3|7704:ZBTB16|5894:RAF1|5914:RARA|5371:PML|3728:JUP|2475:MTOR|1050:CEBPA|51176:LEF1|1978:EIF4EBP1|572:BAD|11040:PIM2|5605:MAP2K2|673:BRAF|5604:MAP2K1|3815:KIT|2322:FLT3|6688:SPI1|3551:IKBKB|207:AKT1|208:AKT2|6198:RPS6KB1|4893:NRAS|10000:AKT3|6199:RPS6KB2|652671:LOC652671|2885:GRB2|6777:STAT5B|5595:MAPK3|6932:TCF7|6776:STAT5A|4790:NFKB1|4609:MYC|6654:SOS1|6934:TCF7L2|5594:MAPK1|861:RUNX1|23533:PIK3R5|8517:IKBKG|3265:HRAS|652799:LOC652799|862:RUNX1T1|5970:RELA|3845:KRAS|652346:LOC652346|8900:CCNA1|369:ARAF|595:CCND1|8503:PIK3R3|83439:TCF7L1|5467:PPARD|5290:PIK3CA|5291:PIK3CB|5292:PIM1|5293:PIK3CD|5294:PIK3CG|5295:PIK3R1|5296:PIK3R2

Any ideas? Thank you

Answer 1

[Cyriac Kandoth]

It is possible that you have a Windows newline (\r\n) instead of Unix (\n). This tends to cause weird problems.

Here is a KEGG pathway file that should work fine. Hope it helps.

[DoubleD]

Thank you for your input! That file was temporarily edited on a Windows machine. Thank you for your example path files, and things are running smoothly now. We also got the original file to work by deleting the headers; I'm sure the \r\n was the culprit