Closed tinypirate08 closed 8 years ago
If somehow you don't have the Font "Arial" installed on your system, then provide the path to something else for the image generation to use for labels. Arial is part of a typical install for Yosemite so I don't know why you wouldn't have it. On your Mac, there should be a bunch of fonts you can list with ls /Library/Fonts/*.ttf
but on CentOS it's probably under /usr/share/fonts/truetype/
I can't really help much with this issue other than pointing out the usage described in the error message.
For example, if you want to use another typical Mac OS X font called Andale Mono:
$ ./lollipops -f="/Library/Fonts/Andale Mono.ttf" -o test.png TAF1 S1579G
HGNC Symbol: TAF1
Uniprot returned 46 hits for your gene symbol 'TAF1':
Entry Entry name Status Gene names Organism
P04637 P53_HUMAN reviewed TP53 P53 Homo sapiens (Human)
P21675 TAF1_HUMAN reviewed TAF1 BA2R CCG1 CCGS TAF2A Homo sapiens (Human)
Q01105 SET_HUMAN reviewed SET Homo sapiens (Human)
P06400 RB_HUMAN reviewed RB1 Homo sapiens (Human)
Q03164 KMT2A_HUMAN reviewed KMT2A ALL1 CXXC7 HRX HTRX MLL MLL1 TRX1 Homo sapiens (Human)
P51610 HCFC1_HUMAN reviewed HCFC1 HCF1 HFC1 Homo sapiens (Human)
Q9Y230 RUVB2_HUMAN reviewed RUVBL2 INO80J TIP48 TIP49B CGI-46 Homo sapiens (Human)
Q15545 TAF7_HUMAN reviewed TAF7 TAF2F TAFII55 Homo sapiens (Human)
Q9Y265 RUVB1_HUMAN reviewed RUVBL1 INO80H NMP238 TIP49 TIP49A Homo sapiens (Human)
P52655 TF2AA_HUMAN reviewed GTF2A1 TF2A1 Homo sapiens (Human)
Q99496 RING2_HUMAN reviewed RNF2 BAP1 DING HIPI3 RING1B Homo sapiens (Human)
Q9HCK8 CHD8_HUMAN reviewed CHD8 HELSNF1 KIAA1564 Homo sapiens (Human)
Q16594 TAF9_HUMAN reviewed TAF9 TAF2G TAFII31 Homo sapiens (Human)
P20226 TBP_HUMAN reviewed TBP GTF2D1 TF2D TFIID Homo sapiens (Human)
Q8IZX4 TAF1L_HUMAN reviewed TAF1L Homo sapiens (Human)
Q9H7Z6 KAT8_HUMAN reviewed KAT8 MOF MYST1 PP7073 Homo sapiens (Human)
Q53T94 TAF1B_HUMAN reviewed TAF1B Homo sapiens (Human)
P61244 MAX_HUMAN reviewed MAX BHLHD4 Homo sapiens (Human)
Q9Y294 ASF1A_HUMAN reviewed ASF1A CGI-98 HSPC146 Homo sapiens (Human)
P35269 T2FA_HUMAN reviewed GTF2F1 RAP74 Homo sapiens (Human)
P61964 WDR5_HUMAN reviewed WDR5 BIG3 Homo sapiens (Human)
Q8WWY3 PRP31_HUMAN reviewed PRPF31 PRP31 Homo sapiens (Human)
P49848 TAF6_HUMAN reviewed TAF6 TAF2E TAFII70 Homo sapiens (Human)
Q96EZ8 MCRS1_HUMAN reviewed MCRS1 INO80Q MSP58 Homo sapiens (Human)
Q9UBL3 ASH2L_HUMAN reviewed ASH2L ASH2L1 Homo sapiens (Human)
Q7Z3B3 KANL1_HUMAN reviewed KANSL1 CENP-36 KIAA1267 MSL1V1 NSL1 Homo sapiens (Human)
Q96IU4 ABHEB_HUMAN reviewed ABHD14B CIB Homo sapiens (Human)
Q9NVP2 ASF1B_HUMAN reviewed ASF1B Homo sapiens (Human)
O75461 E2F6_HUMAN reviewed E2F6 Homo sapiens (Human)
Q9Y262 EIF3L_HUMAN reviewed EIF3L EIF3EIP EIF3S6IP HSPC021 HSPC025 MSTP005 Homo sapiens (Human)
Q6PI98 IN80C_HUMAN reviewed INO80C C18orf37 Homo sapiens (Human)
Q9Y4W2 LAS1L_HUMAN reviewed LAS1L MSTP060 Homo sapiens (Human)
Q8IWI9 MGAP_HUMAN reviewed MGA KIAA0518 MAD5 Homo sapiens (Human)
Q8IZL8 PELP1_HUMAN reviewed PELP1 HMX3 MNAR Homo sapiens (Human)
Q9BVI0 PHF20_HUMAN reviewed PHF20 C20orf104 GLEA2 HCA58 NZF TZP Homo sapiens (Human)
Q15291 RBBP5_HUMAN reviewed RBBP5 RBQ3 Homo sapiens (Human)
Q3B726 RPA43_HUMAN reviewed TWISTNB Homo sapiens (Human)
Q9NYV6 RRN3_HUMAN reviewed RRN3 TIFIA Homo sapiens (Human)
Q9H4L4 SENP3_HUMAN reviewed SENP3 SSP3 SUSP3 Homo sapiens (Human)
Q15542 TAF5_HUMAN reviewed TAF5 TAF2D Homo sapiens (Human)
Q7Z7C8 TAF8_HUMAN reviewed TAF8 TAFII43 TBN Homo sapiens (Human)
Q5H9L4 TAF7L_HUMAN reviewed TAF7L TAF2Q Homo sapiens (Human)
O00268 TAF4_HUMAN reviewed TAF4 TAF2C TAF2C1 TAF4A TAFII130 TAFII135 Homo sapiens (Human)
Q9NXF1 TEX10_HUMAN reviewed TEX10 L18 Nbla10363 Homo sapiens (Human)
Selected 'Q53T94' as the best match. Use -U XXX to use another ID.
Uniprot/SwissProt Accession: Q53T94
Drawing diagram to test.png
You probably don't want the default selection there, use the appropriate Uniprot ID (with -U XXXX):
$ ./lollipops -f="/Library/Fonts/Andale Mono.ttf" -o test.png -U P21675 S1579G
Pfam Symbol: TAF1_HUMAN
Drawing diagram to test.png
Love it! It works now. Thanks for the advice. The plot is amazing!
Hi Jeremy, One quick question. Is there a way to control the domain name labels within the colored domain bars?
What if I did not want to include the text? Looks like if I adjust image size, the text gets truncated within domains. See green and blue bars before and after.
Is there a way to adjust text size, or not to include?
I used command for TAF1.png ./lollipops -f=/Library/Fonts/Courier\ New.ttf -labels -hide-motifs -o TAF1.png -U P21675 S1579G
I used the follwing for TAF1_2.png /lollipops -f=/Library/Fonts/Courier\ New.ttf -labels -hide-motifs -w 6000-dpi 300 -o TAF1_2.png -U P21675 S1579G
I tried multiple size combinations but, there is always one domain name that is truncated.
Thanks for your input. Szabi
[cid:0B472A7B-C1D8-4ECC-9401-98B18832C28E@ad.tgen.org]
[cid:6D5F3841-C363-4D15-96B3-FEEF26D79ECC@ad.tgen.org]
Szabolcs Szelinger, Ph.D Staff Scientist Neurogenomics Division, The Translational Genomics Research Institute (TGen) 445 N. 5th Street, Phoenix AZ 85044 ph:602-343-8723 sszelinger@tgen.orgmailto:sszelinger@tgen.org
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On Feb 1, 2016, at 14:03, Jeremy Jay notifications@github.com<mailto:notifications@github.com> wrote:
Closed #13https://github.com/pbnjay/lollipops/issues/13.
— Reply to this email directly or view it on GitHubhttps://github.com/pbnjay/lollipops/issues/13#event-534824652.
Hi I tried this handy littke thing on both Mac with Yosemite 10.10.5 and on my CentOS 6.6 box. I downloaded the binaries and started with a simple command for a single gene.
I am getting the same error on both.
-bash-4.1$ ./lollipops TAF1 S1579G ERROR: Unable to find Arial.ttf - Required for accurate font sizing. Please use -f=/path/to/arial.ttf or the TTF font of your choice.
Any ideas what may be going on? Thanks