assembly -> chado analysis mapping: we need to download FTP stuff...

[bradfordcondon]

child of #15

assembly has core field information for analysis (algorith namely) in the FTP file. so, we need to

• write an fTP class
• fetch the files, search for the algorithm info.

[bradfordcondon]

heres where the FTP info is parsed into:

tripal_eutils/includes/xml_parsers/EUtilsAssemblyParser.inc

Lines 86 to 88 in cb58726

	case 'FtpSites':
	$list['files'] = $this->processFinalChildren($child, ['type']);
	case 'default':

[bradfordcondon]

<FtpSites>   <FtpPath type="Assembly_rpt">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/285/GCF_000002285.3_CanFam3.1/GCF_000002285.3_CanFam3.1_assembly_report.txt</FtpPath>   <FtpPath type="GenBank">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/285/GCA_000002285.2_CanFam3.1</FtpPath>   <FtpPath type="RefSeq">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/285/GCF_000002285.3_CanFam3.1</FtpPath>   <FtpPath type="Stats_rpt">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/285/GCF_000002285.3_CanFam3.1/GCF_000002285.3_CanFam3.1_assembly_stats.txt</FtpPath> </FtpSites> 

lets consider each of these:

Assembly_rpt
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/285/GCF_000002285.3_CanFam3.1/GCF_000002285.3_CanFam3.1_assembly_report.txt

probably what we want.

refseq:
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/285/GCA_000002285.2_CanFam3.1

directory. handy to show to users, we wont be querying it.

stats report
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/285/GCF_000002285.3_CanFam3.1/GCF_000002285.3_CanFam3.1_assembly_stats.txt

greatly expanded stats report beyond whats included in the CDATA.

so the assembly_rpt is the clear winner.

[bradfordcondon]

heres what we fetch from assembly method in our sample dataset.

 ["# Assembly method:"]=>
  array(1) {
    [0]=>
    string(68) "FALCON v. 0.5.0; Arcs v. 1.0.1; Links v. 1.8.5; BioNano Solve v. 3.1"
  }
}
.array(1) {
  ["# Assembly method:"]=>
  array(1) {
    [0]=>
    string(15) "FALCON v. 0.4.0"
  }
}
.array(1) {
  ["# Assembly method:"]=>
  array(1) {
    [0]=>
    string(21) "Arachne v. April 2010"
  }
}
.array(1) {
  ["# Assembly method:"]=>
  array(1) {
    [0]=>
    string(18) "SOAPdenovo v. 1.14"
  }
}
.array(1) {
  ["# Assembly method:"]=>
  array(1) {
    [0]=>
    string(28) "Celera Assembler (CA) v. 5.3"
  }
}
.array(1) {
  ["# Assembly method:"]=>
  array(1) {
    [0]=>
    string(14) "MaSuRCA v. 2.3"
  }
}
.array(1) {
  ["# Assembly method:"]=>
  array(1) {
    [0]=>
    string(17) "SOAPdenovo v. 1.1"
  }
}
.array(1) {
  ["# Assembly method:"]=>
  array(1) {
    [0]=>
    string(18) "SOAPdenovo v. 1.05"
  }

in the case of single versions, we could totally parse on v. For multiples, we could parse on ;, then parse on v, but im not sure its worth it since hte versions get separated from the programs.

[bradfordcondon]

handled. program and programversion are the same and the full string in assembly method.